Japan is best seen via train. From the super fast shinkansen trains (
http://en.wikipedia.org/wiki/Shinkansen ) to the local milk runs, you can get almost anywhere in Japan by train. They run on time, they run well, and they are priced pretty reasonably. Pretty much everywhere you go in Japan will be mapped relative to a local train station.
Speaking of which, if you are in Tokyo (and many other places) remember that street addresses are essentially useless. The Japanese addressing system (
http://en.wikipedia.org/wiki/Japanese_addressing_system ) means that buildings are often numbered in the order they a built, not in the order they appear on the street. Always get a map, and don't be shy to ask directions, pretty much everyone does.
My best Japan recommendation is EAT. Japanese people love food, there are plenty of different types of food, and tons of great places to eat. From 90yen a piece automated sushi places to bank account emptying steak houses, they have it all.